Abstract

Global climate change intensifies drought threats to wheat productivity, necessitating genetic enhancement of drought resistance. We present a high-quality genome assembly of drought-resistant wheat genotype Jin50LP82 (JIN50; contig N50 = 50.24 Mb) and conduct genomic analyses across 31 wheat genomes and 196 germplasm samples, revealing 430,739 structural variants. Integrated structural variant-, single-nucleotide polymorphism- and InDel-based genome-wide association study identified 46 drought-resistance loci enriched in JIN50. Notably, the structural variation in the promoter of the root development regulator TaLBD1 and functional haplotypes of the methylglyoxal detoxification enzyme TaGLYI7 contribute to drought adaptation through distinct mechanisms. The JIN50 genome and genetic resources provide valuable tools for elucidating drought-resistance networks and for facilitating molecular breeding. These findings contribute to a better understanding of the multigenic drought response system in wheat and support the development of genomic strategies to enhance food security amid climate challenges.